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Yorodumi- PDB-3o2k: Crystal Structure of Brevianamide F Prenyltransferase Complexed w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3o2k | |||||||||
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Title | Crystal Structure of Brevianamide F Prenyltransferase Complexed with Brevianamide F and Dimethylallyl S-thiolodiphosphate | |||||||||
Components | Brevianamide F prenyltransferase | |||||||||
Keywords | TRANSFERASE / PT Barrel / Brevianamide F Prenyltransferase | |||||||||
Function / homology | Function and homology information tryprostatin B synthase / tryptophanyl aminopeptidase / verruculogen biosynthetic process / prenyltransferase activity / aminopeptidase activity / proteolysis Similarity search - Function | |||||||||
Biological species | Aspergillus fumigatus (mold) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Jost, M. / Zocher, G.E. / Stehle, T. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2010 Title: Structure-function analysis of an enzymatic prenyl transfer reaction identifies a reaction chamber with modifiable specificity. Authors: Jost, M. / Zocher, G. / Tarcz, S. / Matuschek, M. / Xie, X. / Li, S.M. / Stehle, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o2k.cif.gz | 186.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o2k.ent.gz | 147.7 KB | Display | PDB format |
PDBx/mmJSON format | 3o2k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o2/3o2k ftp://data.pdbj.org/pub/pdb/validation_reports/o2/3o2k | HTTPS FTP |
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-Related structure data
Related structure data | 3o24SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 53898.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: ftmPT1 / Plasmid: pQE70 / Production host: Escherichia coli (E. coli) / Strain (production host): XL-1 Blue MRF / References: UniProt: Q4G2I1, UniProt: Q4WAW7*PLUS |
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-Non-polymers , 5 types, 51 molecules
#2: Chemical | ChemComp-DST / | ||
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#3: Chemical | ChemComp-QRP / ( | ||
#4: Chemical | ChemComp-MES / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.3M ammonium sulfate, 0.2M lithium sulfate, 0.1M MES, VAPOR DIFFUSION, HANGING DROP. Stepwise transferred to 1.3M lithium sulfate, 0.1M MES pH 6.5, 2.5mM brevianamide F, 10mM dimethylallyl ...Details: 1.3M ammonium sulfate, 0.2M lithium sulfate, 0.1M MES, VAPOR DIFFUSION, HANGING DROP. Stepwise transferred to 1.3M lithium sulfate, 0.1M MES pH 6.5, 2.5mM brevianamide F, 10mM dimethylallyl S-thiolodiphosphate for soaking, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. all: 17531 / Num. obs: 17518 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 23.6 % / Biso Wilson estimate: 50.1 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.109 / Net I/σ(I): 29.95 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 27 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 8.61 / Num. unique all: 1258 / Rsym value: 0.407 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3O24 Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.94 / SU B: 19.944 / SU ML: 0.211 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.574 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.076 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.461 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -19.5448 Å / Origin y: 17.4432 Å / Origin z: 0.9004 Å
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Refinement TLS group |
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